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A critical assessment of gene catalogs for metagenomic analysis

MOTIVATION: Microbial gene catalogs are data structures that organize genes found in microbial communities, providing a reference for standardized analysis of the microbes across samples and studies. Although gene catalogs are commonly used, they have not been critically evaluated for their effectiv...

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Autores principales: Commichaux, Seth, Shah, Nidhi, Ghurye, Jay, Stoppel, Alexander, Goodheart, Jessica A, Luque, Guillermo G, Cummings, Michael P, Pop, Mihai
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8479683/
https://www.ncbi.nlm.nih.gov/pubmed/33792639
http://dx.doi.org/10.1093/bioinformatics/btab216
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author Commichaux, Seth
Shah, Nidhi
Ghurye, Jay
Stoppel, Alexander
Goodheart, Jessica A
Luque, Guillermo G
Cummings, Michael P
Pop, Mihai
author_facet Commichaux, Seth
Shah, Nidhi
Ghurye, Jay
Stoppel, Alexander
Goodheart, Jessica A
Luque, Guillermo G
Cummings, Michael P
Pop, Mihai
author_sort Commichaux, Seth
collection PubMed
description MOTIVATION: Microbial gene catalogs are data structures that organize genes found in microbial communities, providing a reference for standardized analysis of the microbes across samples and studies. Although gene catalogs are commonly used, they have not been critically evaluated for their effectiveness as a basis for metagenomic analyses. RESULTS: As a case study, we investigate one such catalog, the Integrated Gene Catalog (IGC), however, our observations apply broadly to most gene catalogs constructed to date. We focus on both the approach used to construct this catalog and on its effectiveness when used as a reference for microbiome studies. Our results highlight important limitations of the approach used to construct the IGC and call into question the broad usefulness of gene catalogs more generally. We also recommend best practices for the construction and use of gene catalogs in microbiome studies and highlight opportunities for future research. AVAILABILITY AND IMPLEMENTATION: All supporting scripts for our analyses can be found on GitHub: https://github.com/SethCommichaux/IGC.git. The supporting data can be downloaded from: https://obj.umiacs.umd.edu/igc-analysis/IGC_analysis_data.tar.gz. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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spelling pubmed-84796832021-09-30 A critical assessment of gene catalogs for metagenomic analysis Commichaux, Seth Shah, Nidhi Ghurye, Jay Stoppel, Alexander Goodheart, Jessica A Luque, Guillermo G Cummings, Michael P Pop, Mihai Bioinformatics Original Papers MOTIVATION: Microbial gene catalogs are data structures that organize genes found in microbial communities, providing a reference for standardized analysis of the microbes across samples and studies. Although gene catalogs are commonly used, they have not been critically evaluated for their effectiveness as a basis for metagenomic analyses. RESULTS: As a case study, we investigate one such catalog, the Integrated Gene Catalog (IGC), however, our observations apply broadly to most gene catalogs constructed to date. We focus on both the approach used to construct this catalog and on its effectiveness when used as a reference for microbiome studies. Our results highlight important limitations of the approach used to construct the IGC and call into question the broad usefulness of gene catalogs more generally. We also recommend best practices for the construction and use of gene catalogs in microbiome studies and highlight opportunities for future research. AVAILABILITY AND IMPLEMENTATION: All supporting scripts for our analyses can be found on GitHub: https://github.com/SethCommichaux/IGC.git. The supporting data can be downloaded from: https://obj.umiacs.umd.edu/igc-analysis/IGC_analysis_data.tar.gz. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2021-04-01 /pmc/articles/PMC8479683/ /pubmed/33792639 http://dx.doi.org/10.1093/bioinformatics/btab216 Text en © The Author(s) 2021. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Original Papers
Commichaux, Seth
Shah, Nidhi
Ghurye, Jay
Stoppel, Alexander
Goodheart, Jessica A
Luque, Guillermo G
Cummings, Michael P
Pop, Mihai
A critical assessment of gene catalogs for metagenomic analysis
title A critical assessment of gene catalogs for metagenomic analysis
title_full A critical assessment of gene catalogs for metagenomic analysis
title_fullStr A critical assessment of gene catalogs for metagenomic analysis
title_full_unstemmed A critical assessment of gene catalogs for metagenomic analysis
title_short A critical assessment of gene catalogs for metagenomic analysis
title_sort critical assessment of gene catalogs for metagenomic analysis
topic Original Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8479683/
https://www.ncbi.nlm.nih.gov/pubmed/33792639
http://dx.doi.org/10.1093/bioinformatics/btab216
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